Multiple sequence alignment - TraesCS6D01G256500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6D01G256500 chr6D 100.000 2950 0 0 1 2950 362887021 362889970 0.000000e+00 5448.0
1 TraesCS6D01G256500 chr6D 88.011 1101 75 12 971 2029 362859498 362860583 0.000000e+00 1249.0
2 TraesCS6D01G256500 chr6D 85.110 1182 115 37 971 2097 362953831 362955006 0.000000e+00 1151.0
3 TraesCS6D01G256500 chr6D 88.066 905 67 14 972 1840 362634372 362635271 0.000000e+00 1035.0
4 TraesCS6D01G256500 chr6D 93.596 203 5 1 1835 2029 362635372 362635574 2.220000e-76 296.0
5 TraesCS6D01G256500 chr6D 77.800 491 45 28 449 918 362858929 362859376 8.170000e-61 244.0
6 TraesCS6D01G256500 chr6D 81.333 300 22 14 684 965 362953510 362953793 2.300000e-51 213.0
7 TraesCS6D01G256500 chr6D 94.245 139 6 2 2812 2950 165454547 165454411 8.280000e-51 211.0
8 TraesCS6D01G256500 chr6D 93.007 143 8 2 2808 2950 135767601 135767461 1.070000e-49 207.0
9 TraesCS6D01G256500 chr6D 85.714 210 14 5 236 444 362942750 362942944 1.070000e-49 207.0
10 TraesCS6D01G256500 chr6D 94.505 91 2 1 465 555 362953351 362953438 1.430000e-28 137.0
11 TraesCS6D01G256500 chr6A 90.147 1695 67 37 327 1954 503229321 503230982 0.000000e+00 2113.0
12 TraesCS6D01G256500 chr6A 84.429 1567 131 47 440 1953 503248206 503249712 0.000000e+00 1437.0
13 TraesCS6D01G256500 chr6A 89.767 1114 82 18 971 2058 502929035 502930142 0.000000e+00 1397.0
14 TraesCS6D01G256500 chr6A 90.462 325 18 7 15 333 503228698 503229015 1.640000e-112 416.0
15 TraesCS6D01G256500 chr6A 94.286 105 6 0 15 119 503246727 503246831 8.460000e-36 161.0
16 TraesCS6D01G256500 chr6A 90.323 62 4 1 2038 2097 503231708 503231769 2.440000e-11 80.5
17 TraesCS6D01G256500 chr6A 94.118 51 3 0 1979 2029 503231045 503231095 8.770000e-11 78.7
18 TraesCS6D01G256500 chr6B 83.134 1672 113 73 440 2029 544091562 544093146 0.000000e+00 1369.0
19 TraesCS6D01G256500 chr6B 88.717 1099 74 17 972 2029 543825546 543826635 0.000000e+00 1297.0
20 TraesCS6D01G256500 chr6B 86.760 861 75 23 970 1808 543940119 543940962 0.000000e+00 922.0
21 TraesCS6D01G256500 chr6B 84.884 344 34 12 14 355 543908837 543909164 6.090000e-87 331.0
22 TraesCS6D01G256500 chr6B 80.659 455 42 25 455 890 543909627 543910054 7.940000e-81 311.0
23 TraesCS6D01G256500 chr6B 88.053 226 19 6 1808 2029 543959893 543960114 8.110000e-66 261.0
24 TraesCS6D01G256500 chr6B 97.521 121 3 0 2830 2950 694014805 694014685 1.070000e-49 207.0
25 TraesCS6D01G256500 chr6B 85.128 195 21 6 15 201 544091298 544091492 3.000000e-45 193.0
26 TraesCS6D01G256500 chr3D 96.721 732 11 6 2110 2829 598899573 598900303 0.000000e+00 1206.0
27 TraesCS6D01G256500 chr3D 95.219 732 22 4 2110 2829 388797890 388798620 0.000000e+00 1146.0
28 TraesCS6D01G256500 chr3D 97.600 125 3 0 2826 2950 71166237 71166113 6.400000e-52 215.0
29 TraesCS6D01G256500 chr3D 95.489 133 4 2 2820 2950 190089296 190089428 8.280000e-51 211.0
30 TraesCS6D01G256500 chr3D 94.286 70 4 0 1769 1838 1749758 1749827 1.120000e-19 108.0
31 TraesCS6D01G256500 chr1D 95.765 732 18 4 2110 2829 9580966 9581696 0.000000e+00 1168.0
32 TraesCS6D01G256500 chr1D 95.219 732 18 7 2110 2829 467112421 467113147 0.000000e+00 1142.0
33 TraesCS6D01G256500 chr4A 95.753 730 20 4 2110 2829 585436780 585436052 0.000000e+00 1166.0
34 TraesCS6D01G256500 chr4A 94.809 732 24 5 2110 2829 153048331 153047602 0.000000e+00 1129.0
35 TraesCS6D01G256500 chr2D 95.387 737 16 6 2110 2829 8330374 8331109 0.000000e+00 1157.0
36 TraesCS6D01G256500 chr1A 95.212 731 24 4 2110 2829 487483299 487484029 0.000000e+00 1146.0
37 TraesCS6D01G256500 chr7D 95.199 729 23 6 2112 2829 131320313 131321040 0.000000e+00 1142.0
38 TraesCS6D01G256500 chr7D 95.075 731 23 6 2110 2829 63877805 63877077 0.000000e+00 1138.0
39 TraesCS6D01G256500 chr7D 94.617 483 14 3 2110 2580 74943911 74944393 0.000000e+00 737.0
40 TraesCS6D01G256500 chr7D 96.875 128 4 0 2823 2950 208231581 208231708 6.400000e-52 215.0
41 TraesCS6D01G256500 chr7D 94.815 135 7 0 2816 2950 622300522 622300388 8.280000e-51 211.0
42 TraesCS6D01G256500 chr5B 94.945 732 23 5 2110 2829 712869120 712869849 0.000000e+00 1134.0
43 TraesCS6D01G256500 chr5B 94.118 731 30 6 2110 2829 9577792 9578520 0.000000e+00 1099.0
44 TraesCS6D01G256500 chr5D 94.918 728 25 7 2113 2829 77441574 77440848 0.000000e+00 1129.0
45 TraesCS6D01G256500 chrUn 92.556 403 17 6 2110 2500 74706127 74706528 1.530000e-157 566.0
46 TraesCS6D01G256500 chr7B 95.522 134 3 3 2819 2950 658811630 658811498 8.280000e-51 211.0
47 TraesCS6D01G256500 chr2A 88.415 164 14 5 2787 2950 349953187 349953345 3.000000e-45 193.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G256500 chr6D 362887021 362889970 2949 False 5448.000000 5448 100.000000 1 2950 1 chr6D.!!$F1 2949
1 TraesCS6D01G256500 chr6D 362858929 362860583 1654 False 746.500000 1249 82.905500 449 2029 2 chr6D.!!$F4 1580
2 TraesCS6D01G256500 chr6D 362634372 362635574 1202 False 665.500000 1035 90.831000 972 2029 2 chr6D.!!$F3 1057
3 TraesCS6D01G256500 chr6D 362953351 362955006 1655 False 500.333333 1151 86.982667 465 2097 3 chr6D.!!$F5 1632
4 TraesCS6D01G256500 chr6A 502929035 502930142 1107 False 1397.000000 1397 89.767000 971 2058 1 chr6A.!!$F1 1087
5 TraesCS6D01G256500 chr6A 503246727 503249712 2985 False 799.000000 1437 89.357500 15 1953 2 chr6A.!!$F3 1938
6 TraesCS6D01G256500 chr6A 503228698 503231769 3071 False 672.050000 2113 91.262500 15 2097 4 chr6A.!!$F2 2082
7 TraesCS6D01G256500 chr6B 543825546 543826635 1089 False 1297.000000 1297 88.717000 972 2029 1 chr6B.!!$F1 1057
8 TraesCS6D01G256500 chr6B 543940119 543940962 843 False 922.000000 922 86.760000 970 1808 1 chr6B.!!$F2 838
9 TraesCS6D01G256500 chr6B 544091298 544093146 1848 False 781.000000 1369 84.131000 15 2029 2 chr6B.!!$F5 2014
10 TraesCS6D01G256500 chr6B 543908837 543910054 1217 False 321.000000 331 82.771500 14 890 2 chr6B.!!$F4 876
11 TraesCS6D01G256500 chr3D 598899573 598900303 730 False 1206.000000 1206 96.721000 2110 2829 1 chr3D.!!$F4 719
12 TraesCS6D01G256500 chr3D 388797890 388798620 730 False 1146.000000 1146 95.219000 2110 2829 1 chr3D.!!$F3 719
13 TraesCS6D01G256500 chr1D 9580966 9581696 730 False 1168.000000 1168 95.765000 2110 2829 1 chr1D.!!$F1 719
14 TraesCS6D01G256500 chr1D 467112421 467113147 726 False 1142.000000 1142 95.219000 2110 2829 1 chr1D.!!$F2 719
15 TraesCS6D01G256500 chr4A 585436052 585436780 728 True 1166.000000 1166 95.753000 2110 2829 1 chr4A.!!$R2 719
16 TraesCS6D01G256500 chr4A 153047602 153048331 729 True 1129.000000 1129 94.809000 2110 2829 1 chr4A.!!$R1 719
17 TraesCS6D01G256500 chr2D 8330374 8331109 735 False 1157.000000 1157 95.387000 2110 2829 1 chr2D.!!$F1 719
18 TraesCS6D01G256500 chr1A 487483299 487484029 730 False 1146.000000 1146 95.212000 2110 2829 1 chr1A.!!$F1 719
19 TraesCS6D01G256500 chr7D 131320313 131321040 727 False 1142.000000 1142 95.199000 2112 2829 1 chr7D.!!$F2 717
20 TraesCS6D01G256500 chr7D 63877077 63877805 728 True 1138.000000 1138 95.075000 2110 2829 1 chr7D.!!$R1 719
21 TraesCS6D01G256500 chr5B 712869120 712869849 729 False 1134.000000 1134 94.945000 2110 2829 1 chr5B.!!$F2 719
22 TraesCS6D01G256500 chr5B 9577792 9578520 728 False 1099.000000 1099 94.118000 2110 2829 1 chr5B.!!$F1 719
23 TraesCS6D01G256500 chr5D 77440848 77441574 726 True 1129.000000 1129 94.918000 2113 2829 1 chr5D.!!$R1 716

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
814 2661 0.241481 ACGCACGGTGTTTTGTTTGT 59.759 45.000 10.24 0.00 0.00 2.83 F
816 2663 1.319079 CGCACGGTGTTTTGTTTGTTC 59.681 47.619 10.24 0.00 0.00 3.18 F
1149 3105 2.030562 GGCTATGCGTACGCCCAT 59.969 61.111 35.11 25.06 41.09 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 3681 0.938008 GATCCTCCGAAATCCGCAAC 59.062 55.0 0.00 0.0 36.84 4.17 R
1936 4078 2.042686 AGCAGTTCAGTTCAGTTGCA 57.957 45.0 0.00 0.0 34.17 4.08 R
2863 5671 0.036164 TTGTCTGGTGCGCCATTAGT 59.964 50.0 21.54 0.0 45.05 2.24 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 4.088823 GCAAAGGCTCTATGTGTTCTTG 57.911 45.455 0.00 0.00 36.96 3.02
120 121 3.119708 GCAAAGGCTCTATGTGTTCTTGG 60.120 47.826 0.00 0.00 36.96 3.61
226 227 4.603131 AGAGAGGGCAATGCAAATAAGAA 58.397 39.130 7.79 0.00 0.00 2.52
228 229 4.347607 AGAGGGCAATGCAAATAAGAAGT 58.652 39.130 7.79 0.00 0.00 3.01
229 230 5.509498 AGAGGGCAATGCAAATAAGAAGTA 58.491 37.500 7.79 0.00 0.00 2.24
230 231 5.591877 AGAGGGCAATGCAAATAAGAAGTAG 59.408 40.000 7.79 0.00 0.00 2.57
231 232 4.646492 AGGGCAATGCAAATAAGAAGTAGG 59.354 41.667 7.79 0.00 0.00 3.18
232 233 4.644685 GGGCAATGCAAATAAGAAGTAGGA 59.355 41.667 7.79 0.00 0.00 2.94
233 234 5.221126 GGGCAATGCAAATAAGAAGTAGGAG 60.221 44.000 7.79 0.00 0.00 3.69
234 235 5.358160 GGCAATGCAAATAAGAAGTAGGAGT 59.642 40.000 7.79 0.00 0.00 3.85
240 241 8.492673 TGCAAATAAGAAGTAGGAGTATGTTG 57.507 34.615 0.00 0.00 0.00 3.33
288 293 8.292448 ACTGCTTCTACAATATTTTCACACTTG 58.708 33.333 0.00 0.00 0.00 3.16
296 301 3.904136 ATTTTCACACTTGAAGGAGCG 57.096 42.857 0.00 0.00 42.79 5.03
394 1127 5.964168 CGTTGTACGAGTAGGAAATGTAGAG 59.036 44.000 0.00 0.00 46.05 2.43
404 1137 7.339482 AGTAGGAAATGTAGAGAACCCATTTC 58.661 38.462 13.28 13.28 46.99 2.17
413 1146 1.818674 AGAACCCATTTCCGTTGCATC 59.181 47.619 0.00 0.00 34.32 3.91
446 1873 2.125952 GGGCAAGGCAAATCGCAC 60.126 61.111 0.00 0.00 45.17 5.34
507 2328 4.124943 AGAGCCCGTCGCCTCCTA 62.125 66.667 7.31 0.00 38.78 2.94
588 2409 0.749454 ATTTCAGCTGGATCCGCACC 60.749 55.000 24.07 6.93 0.00 5.01
589 2410 2.819984 TTTCAGCTGGATCCGCACCC 62.820 60.000 24.07 5.37 0.00 4.61
633 2454 2.092212 TCCCTTCCTTCATGCATTCCTC 60.092 50.000 0.00 0.00 0.00 3.71
635 2456 2.950309 CCTTCCTTCATGCATTCCTCTG 59.050 50.000 0.00 0.00 0.00 3.35
750 2590 1.486310 TCGGCAGCTCAATCACCTATT 59.514 47.619 0.00 0.00 0.00 1.73
812 2659 0.456995 CCACGCACGGTGTTTTGTTT 60.457 50.000 10.24 0.00 45.52 2.83
813 2660 0.637738 CACGCACGGTGTTTTGTTTG 59.362 50.000 10.24 0.00 41.89 2.93
814 2661 0.241481 ACGCACGGTGTTTTGTTTGT 59.759 45.000 10.24 0.00 0.00 2.83
815 2662 1.336056 ACGCACGGTGTTTTGTTTGTT 60.336 42.857 10.24 0.00 0.00 2.83
816 2663 1.319079 CGCACGGTGTTTTGTTTGTTC 59.681 47.619 10.24 0.00 0.00 3.18
1034 2990 3.576356 GCCGATGGTGATGTGCGG 61.576 66.667 0.00 0.00 44.47 5.69
1149 3105 2.030562 GGCTATGCGTACGCCCAT 59.969 61.111 35.11 25.06 41.09 4.00
1488 3486 2.389866 GATCGTACGCGGACCAGGAG 62.390 65.000 17.51 0.61 38.89 3.69
1648 3668 8.948631 TCTTTCTACTGCTCGAATTCATTATT 57.051 30.769 6.22 0.00 0.00 1.40
1660 3681 6.410625 TCGAATTCATTATTCATTGCGTTTCG 59.589 34.615 6.22 0.00 42.34 3.46
1664 3685 4.556912 TCATTATTCATTGCGTTTCGTTGC 59.443 37.500 0.00 0.00 0.00 4.17
1936 4078 1.338337 CATCTTATCGTCGCAGAGGGT 59.662 52.381 0.00 0.00 43.36 4.34
1998 4178 8.755941 CAAACGTATGGTAGAGATTAATCAGTG 58.244 37.037 17.56 0.00 0.00 3.66
2029 4209 6.040878 CACCTCGTTCGAAGATAAATAAGGT 58.959 40.000 0.00 0.26 35.04 3.50
2030 4210 6.534079 CACCTCGTTCGAAGATAAATAAGGTT 59.466 38.462 0.00 0.00 35.04 3.50
2031 4211 6.534079 ACCTCGTTCGAAGATAAATAAGGTTG 59.466 38.462 0.00 0.00 35.04 3.77
2033 4213 5.005012 TCGTTCGAAGATAAATAAGGTTGCG 59.995 40.000 0.00 0.00 35.04 4.85
2034 4214 4.789095 TCGAAGATAAATAAGGTTGCGC 57.211 40.909 0.00 0.00 0.00 6.09
2035 4215 4.439057 TCGAAGATAAATAAGGTTGCGCT 58.561 39.130 9.73 0.00 0.00 5.92
2036 4216 5.593968 TCGAAGATAAATAAGGTTGCGCTA 58.406 37.500 9.73 0.00 0.00 4.26
2040 4824 9.297586 CGAAGATAAATAAGGTTGCGCTATATA 57.702 33.333 9.73 0.00 0.00 0.86
2079 4865 5.139001 TGATGCAGTGATGTAGAGAGAGAT 58.861 41.667 0.00 0.00 0.00 2.75
2080 4866 6.302269 TGATGCAGTGATGTAGAGAGAGATA 58.698 40.000 0.00 0.00 0.00 1.98
2231 5018 0.606673 GCCCGAGAAACCTGCTTCTT 60.607 55.000 0.00 0.00 35.76 2.52
2342 5129 3.535280 TCGTATGCAAGTTATCAGGCA 57.465 42.857 0.00 0.00 41.00 4.75
2829 5637 9.630098 CCATCATGTTTATATTGCAAGTTATCC 57.370 33.333 4.94 0.00 0.00 2.59
2832 5640 9.407380 TCATGTTTATATTGCAAGTTATCCACT 57.593 29.630 4.94 0.00 37.30 4.00
2835 5643 9.899661 TGTTTATATTGCAAGTTATCCACTACT 57.100 29.630 4.94 0.00 32.94 2.57
2842 5650 8.911918 TTGCAAGTTATCCACTACTAGAAAAA 57.088 30.769 0.00 0.00 32.94 1.94
2843 5651 8.547967 TGCAAGTTATCCACTACTAGAAAAAG 57.452 34.615 0.00 0.00 32.94 2.27
2844 5652 8.372459 TGCAAGTTATCCACTACTAGAAAAAGA 58.628 33.333 0.00 0.00 32.94 2.52
2845 5653 8.874816 GCAAGTTATCCACTACTAGAAAAAGAG 58.125 37.037 0.00 0.00 32.94 2.85
2846 5654 8.874816 CAAGTTATCCACTACTAGAAAAAGAGC 58.125 37.037 0.00 0.00 32.94 4.09
2847 5655 8.368962 AGTTATCCACTACTAGAAAAAGAGCT 57.631 34.615 0.00 0.00 31.97 4.09
2848 5656 9.476928 AGTTATCCACTACTAGAAAAAGAGCTA 57.523 33.333 0.00 0.00 31.97 3.32
2852 5660 9.869667 ATCCACTACTAGAAAAAGAGCTATAGA 57.130 33.333 3.21 0.00 0.00 1.98
2853 5661 9.869667 TCCACTACTAGAAAAAGAGCTATAGAT 57.130 33.333 3.21 0.00 0.00 1.98
2854 5662 9.906660 CCACTACTAGAAAAAGAGCTATAGATG 57.093 37.037 3.21 0.00 0.00 2.90
2862 5670 9.762933 AGAAAAAGAGCTATAGATGAGATTGAC 57.237 33.333 3.21 0.00 0.00 3.18
2863 5671 9.539825 GAAAAAGAGCTATAGATGAGATTGACA 57.460 33.333 3.21 0.00 0.00 3.58
2864 5672 8.885494 AAAAGAGCTATAGATGAGATTGACAC 57.115 34.615 3.21 0.00 0.00 3.67
2865 5673 7.838079 AAGAGCTATAGATGAGATTGACACT 57.162 36.000 3.21 0.00 0.00 3.55
2866 5674 8.932434 AAGAGCTATAGATGAGATTGACACTA 57.068 34.615 3.21 0.00 0.00 2.74
2867 5675 8.932434 AGAGCTATAGATGAGATTGACACTAA 57.068 34.615 3.21 0.00 0.00 2.24
2868 5676 9.532494 AGAGCTATAGATGAGATTGACACTAAT 57.468 33.333 3.21 0.00 0.00 1.73
2869 5677 9.571810 GAGCTATAGATGAGATTGACACTAATG 57.428 37.037 3.21 0.00 0.00 1.90
2870 5678 8.530311 AGCTATAGATGAGATTGACACTAATGG 58.470 37.037 3.21 0.00 0.00 3.16
2871 5679 7.277539 GCTATAGATGAGATTGACACTAATGGC 59.722 40.741 3.21 0.00 0.00 4.40
2872 5680 4.375272 AGATGAGATTGACACTAATGGCG 58.625 43.478 0.00 0.00 36.14 5.69
2873 5681 2.279741 TGAGATTGACACTAATGGCGC 58.720 47.619 0.00 0.00 36.14 6.53
2874 5682 2.279741 GAGATTGACACTAATGGCGCA 58.720 47.619 10.83 0.00 36.14 6.09
2875 5683 2.009774 AGATTGACACTAATGGCGCAC 58.990 47.619 10.83 0.00 36.14 5.34
2876 5684 1.064060 GATTGACACTAATGGCGCACC 59.936 52.381 10.83 0.00 36.14 5.01
2890 5698 3.716006 CACCAGACAAGCGGTGCG 61.716 66.667 0.00 0.00 45.77 5.34
2917 5725 6.593268 TTAGTATATACTAATGGCGCACCA 57.407 37.500 25.06 0.00 42.34 4.17
2918 5726 4.817517 AGTATATACTAATGGCGCACCAC 58.182 43.478 13.88 0.00 41.40 4.16
2919 5727 4.322499 AGTATATACTAATGGCGCACCACC 60.322 45.833 13.88 0.00 41.40 4.61
2920 5728 6.510790 AGTATATACTAATGGCGCACCACCT 61.511 44.000 13.88 0.00 41.40 4.00
2921 5729 7.929446 AGTATATACTAATGGCGCACCACCTT 61.929 42.308 13.88 0.00 41.40 3.50
2922 5730 9.615037 AGTATATACTAATGGCGCACCACCTTC 62.615 44.444 13.88 0.00 41.40 3.46
2925 5733 3.555324 TGGCGCACCACCTTCTGA 61.555 61.111 10.83 0.00 42.67 3.27
2926 5734 2.045926 GGCGCACCACCTTCTGAT 60.046 61.111 10.83 0.00 35.26 2.90
2927 5735 1.220749 GGCGCACCACCTTCTGATA 59.779 57.895 10.83 0.00 35.26 2.15
2928 5736 1.090052 GGCGCACCACCTTCTGATAC 61.090 60.000 10.83 0.00 35.26 2.24
2929 5737 1.421410 GCGCACCACCTTCTGATACG 61.421 60.000 0.30 0.00 0.00 3.06
2930 5738 1.421410 CGCACCACCTTCTGATACGC 61.421 60.000 0.00 0.00 0.00 4.42
2931 5739 1.090052 GCACCACCTTCTGATACGCC 61.090 60.000 0.00 0.00 0.00 5.68
2932 5740 0.249120 CACCACCTTCTGATACGCCA 59.751 55.000 0.00 0.00 0.00 5.69
2933 5741 1.134401 CACCACCTTCTGATACGCCAT 60.134 52.381 0.00 0.00 0.00 4.40
2934 5742 1.559682 ACCACCTTCTGATACGCCATT 59.440 47.619 0.00 0.00 0.00 3.16
2935 5743 2.769663 ACCACCTTCTGATACGCCATTA 59.230 45.455 0.00 0.00 0.00 1.90
2936 5744 3.181465 ACCACCTTCTGATACGCCATTAG 60.181 47.826 0.00 0.00 0.00 1.73
2937 5745 3.069586 CCACCTTCTGATACGCCATTAGA 59.930 47.826 0.00 0.00 0.00 2.10
2938 5746 4.302455 CACCTTCTGATACGCCATTAGAG 58.698 47.826 0.00 0.00 31.43 2.43
2939 5747 3.961408 ACCTTCTGATACGCCATTAGAGT 59.039 43.478 0.00 0.00 31.43 3.24
2940 5748 4.406003 ACCTTCTGATACGCCATTAGAGTT 59.594 41.667 0.00 0.00 31.43 3.01
2941 5749 4.747108 CCTTCTGATACGCCATTAGAGTTG 59.253 45.833 0.00 0.00 31.43 3.16
2942 5750 5.451937 CCTTCTGATACGCCATTAGAGTTGA 60.452 44.000 0.00 0.00 31.43 3.18
2943 5751 5.592104 TCTGATACGCCATTAGAGTTGAA 57.408 39.130 0.00 0.00 0.00 2.69
2944 5752 5.972935 TCTGATACGCCATTAGAGTTGAAA 58.027 37.500 0.00 0.00 0.00 2.69
2945 5753 5.810587 TCTGATACGCCATTAGAGTTGAAAC 59.189 40.000 0.00 0.00 0.00 2.78
2946 5754 5.730550 TGATACGCCATTAGAGTTGAAACT 58.269 37.500 0.00 0.00 43.16 2.66
2947 5755 6.869695 TGATACGCCATTAGAGTTGAAACTA 58.130 36.000 0.00 0.00 39.88 2.24
2948 5756 6.755141 TGATACGCCATTAGAGTTGAAACTAC 59.245 38.462 0.00 0.00 39.88 2.73
2949 5757 5.148651 ACGCCATTAGAGTTGAAACTACT 57.851 39.130 0.00 0.00 39.88 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
190 191 2.301346 CCTCTCTTTATTGCGGCCATT 58.699 47.619 2.24 0.00 0.00 3.16
226 227 9.961264 TCGATAAGATATCAACATACTCCTACT 57.039 33.333 5.32 0.00 0.00 2.57
228 229 9.734984 TGTCGATAAGATATCAACATACTCCTA 57.265 33.333 5.32 0.00 0.00 2.94
229 230 8.516234 GTGTCGATAAGATATCAACATACTCCT 58.484 37.037 5.32 0.00 0.00 3.69
230 231 7.755822 GGTGTCGATAAGATATCAACATACTCC 59.244 40.741 5.32 3.15 0.00 3.85
231 232 7.482113 CGGTGTCGATAAGATATCAACATACTC 59.518 40.741 5.32 0.00 39.00 2.59
232 233 7.174426 TCGGTGTCGATAAGATATCAACATACT 59.826 37.037 5.32 0.00 40.88 2.12
233 234 7.303261 TCGGTGTCGATAAGATATCAACATAC 58.697 38.462 5.32 0.00 40.88 2.39
234 235 7.443259 TCGGTGTCGATAAGATATCAACATA 57.557 36.000 5.32 0.00 40.88 2.29
250 251 1.959899 GAAGCAGTGCATCGGTGTCG 61.960 60.000 19.20 0.00 37.82 4.35
288 293 1.646189 CCTTTGCTAGTCGCTCCTTC 58.354 55.000 0.00 0.00 40.11 3.46
394 1127 1.467374 CGATGCAACGGAAATGGGTTC 60.467 52.381 8.71 0.00 35.28 3.62
413 1146 1.661821 CCCTCTCTTTATCGCGGCG 60.662 63.158 17.70 17.70 0.00 6.46
419 1803 2.717639 TGCCTTGCCCTCTCTTTATC 57.282 50.000 0.00 0.00 0.00 1.75
446 1873 0.179089 CCTCTCTTCTCATGTGGCCG 60.179 60.000 0.00 0.00 0.00 6.13
595 2416 3.527360 GAGGTTGTGTGCGCTGTGC 62.527 63.158 9.73 6.19 46.70 4.57
596 2417 2.633657 GAGGTTGTGTGCGCTGTG 59.366 61.111 9.73 0.00 0.00 3.66
597 2418 2.591715 GGAGGTTGTGTGCGCTGT 60.592 61.111 9.73 0.00 0.00 4.40
598 2419 3.357079 GGGAGGTTGTGTGCGCTG 61.357 66.667 9.73 0.00 0.00 5.18
599 2420 3.120086 AAGGGAGGTTGTGTGCGCT 62.120 57.895 9.73 0.00 0.00 5.92
668 2489 3.877508 CCAAGAACAAATACCGGATCTCC 59.122 47.826 9.46 0.00 0.00 3.71
812 2659 3.267483 GCATAAAGAAGCCGGTAGAACA 58.733 45.455 1.90 0.00 0.00 3.18
813 2660 2.612672 GGCATAAAGAAGCCGGTAGAAC 59.387 50.000 1.90 0.00 41.70 3.01
814 2661 2.914059 GGCATAAAGAAGCCGGTAGAA 58.086 47.619 1.90 0.00 41.70 2.10
815 2662 2.614829 GGCATAAAGAAGCCGGTAGA 57.385 50.000 1.90 0.00 41.70 2.59
876 2735 4.379082 CGCCGGCTATATATATACATGCGA 60.379 45.833 26.68 0.00 39.46 5.10
995 2951 1.559814 CGCACTAACGCCATGATCG 59.440 57.895 0.00 0.00 0.00 3.69
1317 3303 2.505982 CCTATGGTGGACGCTGGG 59.494 66.667 0.00 0.00 0.00 4.45
1505 3503 4.389576 CACCGCACGGCTTCTTGC 62.390 66.667 9.43 0.00 39.32 4.01
1648 3668 1.082431 CCGCAACGAAACGCAATGA 60.082 52.632 0.00 0.00 0.00 2.57
1660 3681 0.938008 GATCCTCCGAAATCCGCAAC 59.062 55.000 0.00 0.00 36.84 4.17
1664 3685 2.474816 GTTCAGATCCTCCGAAATCCG 58.525 52.381 0.00 0.00 38.18 4.18
1936 4078 2.042686 AGCAGTTCAGTTCAGTTGCA 57.957 45.000 0.00 0.00 34.17 4.08
2029 4209 9.874215 GATCAAGTACGTATATATATAGCGCAA 57.126 33.333 11.47 0.00 0.00 4.85
2030 4210 9.269453 AGATCAAGTACGTATATATATAGCGCA 57.731 33.333 11.47 0.00 0.00 6.09
2031 4211 9.531412 CAGATCAAGTACGTATATATATAGCGC 57.469 37.037 17.31 0.00 0.00 5.92
2040 4824 7.040409 TCACTGCATCAGATCAAGTACGTATAT 60.040 37.037 0.00 0.00 35.18 0.86
2045 4829 3.774066 TCACTGCATCAGATCAAGTACG 58.226 45.455 0.29 0.00 35.18 3.67
2097 4883 5.939883 TGCTTATATGGCAATATCACAGTCC 59.060 40.000 0.00 0.00 36.71 3.85
2098 4884 7.439157 TTGCTTATATGGCAATATCACAGTC 57.561 36.000 11.99 0.00 43.50 3.51
2099 4885 7.822161 TTTGCTTATATGGCAATATCACAGT 57.178 32.000 15.30 0.00 46.81 3.55
2100 4886 8.355169 AGTTTTGCTTATATGGCAATATCACAG 58.645 33.333 15.30 0.00 46.81 3.66
2101 4887 8.136800 CAGTTTTGCTTATATGGCAATATCACA 58.863 33.333 15.30 0.00 46.81 3.58
2102 4888 7.115378 GCAGTTTTGCTTATATGGCAATATCAC 59.885 37.037 15.30 11.12 46.81 3.06
2103 4889 7.147312 GCAGTTTTGCTTATATGGCAATATCA 58.853 34.615 15.30 2.48 46.81 2.15
2104 4890 7.572502 GCAGTTTTGCTTATATGGCAATATC 57.427 36.000 15.30 10.39 46.81 1.63
2360 5147 7.104043 TGGTACGTTCTATGTAAATAGCACT 57.896 36.000 0.00 0.00 0.00 4.40
2836 5644 9.762933 GTCAATCTCATCTATAGCTCTTTTTCT 57.237 33.333 0.00 0.00 0.00 2.52
2837 5645 9.539825 TGTCAATCTCATCTATAGCTCTTTTTC 57.460 33.333 0.00 0.00 0.00 2.29
2838 5646 9.323985 GTGTCAATCTCATCTATAGCTCTTTTT 57.676 33.333 0.00 0.00 0.00 1.94
2839 5647 8.703743 AGTGTCAATCTCATCTATAGCTCTTTT 58.296 33.333 0.00 0.00 0.00 2.27
2840 5648 8.248904 AGTGTCAATCTCATCTATAGCTCTTT 57.751 34.615 0.00 0.00 0.00 2.52
2841 5649 7.838079 AGTGTCAATCTCATCTATAGCTCTT 57.162 36.000 0.00 0.00 0.00 2.85
2842 5650 8.932434 TTAGTGTCAATCTCATCTATAGCTCT 57.068 34.615 0.00 0.00 0.00 4.09
2843 5651 9.571810 CATTAGTGTCAATCTCATCTATAGCTC 57.428 37.037 0.00 0.00 0.00 4.09
2844 5652 8.530311 CCATTAGTGTCAATCTCATCTATAGCT 58.470 37.037 0.00 0.00 0.00 3.32
2845 5653 7.277539 GCCATTAGTGTCAATCTCATCTATAGC 59.722 40.741 0.00 0.00 0.00 2.97
2846 5654 7.487509 CGCCATTAGTGTCAATCTCATCTATAG 59.512 40.741 0.00 0.00 0.00 1.31
2847 5655 7.315890 CGCCATTAGTGTCAATCTCATCTATA 58.684 38.462 0.00 0.00 0.00 1.31
2848 5656 6.162079 CGCCATTAGTGTCAATCTCATCTAT 58.838 40.000 0.00 0.00 0.00 1.98
2849 5657 5.532557 CGCCATTAGTGTCAATCTCATCTA 58.467 41.667 0.00 0.00 0.00 1.98
2850 5658 4.375272 CGCCATTAGTGTCAATCTCATCT 58.625 43.478 0.00 0.00 0.00 2.90
2851 5659 3.059325 GCGCCATTAGTGTCAATCTCATC 60.059 47.826 0.00 0.00 0.00 2.92
2852 5660 2.874701 GCGCCATTAGTGTCAATCTCAT 59.125 45.455 0.00 0.00 0.00 2.90
2853 5661 2.279741 GCGCCATTAGTGTCAATCTCA 58.720 47.619 0.00 0.00 0.00 3.27
2854 5662 2.030946 GTGCGCCATTAGTGTCAATCTC 59.969 50.000 4.18 0.00 0.00 2.75
2855 5663 2.009774 GTGCGCCATTAGTGTCAATCT 58.990 47.619 4.18 0.00 0.00 2.40
2856 5664 1.064060 GGTGCGCCATTAGTGTCAATC 59.936 52.381 12.58 0.00 34.09 2.67
2857 5665 1.094785 GGTGCGCCATTAGTGTCAAT 58.905 50.000 12.58 0.00 34.09 2.57
2858 5666 0.250510 TGGTGCGCCATTAGTGTCAA 60.251 50.000 16.89 0.00 40.46 3.18
2859 5667 0.673333 CTGGTGCGCCATTAGTGTCA 60.673 55.000 21.54 0.00 45.05 3.58
2860 5668 0.391130 TCTGGTGCGCCATTAGTGTC 60.391 55.000 21.54 0.00 45.05 3.67
2861 5669 0.673644 GTCTGGTGCGCCATTAGTGT 60.674 55.000 21.54 0.00 45.05 3.55
2862 5670 0.673333 TGTCTGGTGCGCCATTAGTG 60.673 55.000 21.54 7.89 45.05 2.74
2863 5671 0.036164 TTGTCTGGTGCGCCATTAGT 59.964 50.000 21.54 0.00 45.05 2.24
2864 5672 0.729116 CTTGTCTGGTGCGCCATTAG 59.271 55.000 21.54 8.73 45.05 1.73
2865 5673 1.305219 GCTTGTCTGGTGCGCCATTA 61.305 55.000 21.54 8.54 45.05 1.90
2866 5674 2.629656 GCTTGTCTGGTGCGCCATT 61.630 57.895 21.54 0.00 45.05 3.16
2867 5675 3.058160 GCTTGTCTGGTGCGCCAT 61.058 61.111 21.54 0.00 45.05 4.40
2880 5688 7.677982 TAGTATATACTAATAGCGCACCGCTTG 60.678 40.741 18.36 8.36 46.86 4.01
2881 5689 6.317140 TAGTATATACTAATAGCGCACCGCTT 59.683 38.462 18.36 3.28 46.86 4.68
2883 5691 4.918037 AGTATATACTAATAGCGCACCGC 58.082 43.478 13.88 0.69 43.50 5.68
2908 5716 1.549243 TATCAGAAGGTGGTGCGCCA 61.549 55.000 16.89 16.89 43.73 5.69
2909 5717 1.090052 GTATCAGAAGGTGGTGCGCC 61.090 60.000 10.11 10.11 0.00 6.53
2910 5718 1.421410 CGTATCAGAAGGTGGTGCGC 61.421 60.000 0.00 0.00 38.61 6.09
2911 5719 2.665777 CGTATCAGAAGGTGGTGCG 58.334 57.895 0.00 0.00 39.12 5.34
2912 5720 1.090052 GGCGTATCAGAAGGTGGTGC 61.090 60.000 0.00 0.00 0.00 5.01
2913 5721 0.249120 TGGCGTATCAGAAGGTGGTG 59.751 55.000 0.00 0.00 0.00 4.17
2914 5722 1.204146 ATGGCGTATCAGAAGGTGGT 58.796 50.000 0.00 0.00 0.00 4.16
2915 5723 2.332063 AATGGCGTATCAGAAGGTGG 57.668 50.000 0.00 0.00 0.00 4.61
2916 5724 4.202161 ACTCTAATGGCGTATCAGAAGGTG 60.202 45.833 0.00 0.00 0.00 4.00
2917 5725 3.961408 ACTCTAATGGCGTATCAGAAGGT 59.039 43.478 0.00 0.00 0.00 3.50
2918 5726 4.592485 ACTCTAATGGCGTATCAGAAGG 57.408 45.455 0.00 0.00 0.00 3.46
2919 5727 5.592054 TCAACTCTAATGGCGTATCAGAAG 58.408 41.667 0.00 0.00 0.00 2.85
2920 5728 5.592104 TCAACTCTAATGGCGTATCAGAA 57.408 39.130 0.00 0.00 0.00 3.02
2921 5729 5.592104 TTCAACTCTAATGGCGTATCAGA 57.408 39.130 0.00 0.00 0.00 3.27
2922 5730 5.812642 AGTTTCAACTCTAATGGCGTATCAG 59.187 40.000 0.00 0.00 32.86 2.90
2923 5731 5.730550 AGTTTCAACTCTAATGGCGTATCA 58.269 37.500 0.00 0.00 32.86 2.15
2924 5732 6.979238 AGTAGTTTCAACTCTAATGGCGTATC 59.021 38.462 0.00 0.00 40.37 2.24
2925 5733 6.875076 AGTAGTTTCAACTCTAATGGCGTAT 58.125 36.000 0.00 0.00 40.37 3.06
2926 5734 6.276832 AGTAGTTTCAACTCTAATGGCGTA 57.723 37.500 0.00 0.00 40.37 4.42
2927 5735 5.148651 AGTAGTTTCAACTCTAATGGCGT 57.851 39.130 0.00 0.00 40.37 5.68


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.